Differential Expression
Wald Tests
Ectoderm (gd7) vs Mesoderm (Toll10b)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 3626
##
## N U1 U2 U3 D3 D2 D1
## 6029 1157 456 264 244 436 1069
Neuroectoderm (Tollrm9rm10) vs Mesoderm (Toll10b)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 2746
##
## N U1 U2 U3 D3 D2 D1
## 6909 742 434 270 242 282 776
Neuroectoderm (Tollrm9rm10) vs Ectoderm (gd7)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 1193
##
## N U1 U2 U3 D3 D2 D1
## 8487 369 151 119 94 126 334
Likelihood Ratio Test
Number of significant genes (padj < 0.1):
## [1] 4173Session Info
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] EnhancedVolcano_1.8.0 ggrepel_0.9.1
## [3] dplyr_1.0.5 limma_3.46.0
## [5] geneplotter_1.68.0 annotate_1.68.0
## [7] XML_3.99-0.6 reshape_0.8.8
## [9] lattice_0.20-41 ggplot2_3.3.3
## [11] gridExtra_2.3 biomaRt_2.46.3
## [13] gplots_3.1.1 RColorBrewer_1.1-2
## [15] GenomicFeatures_1.42.3 AnnotationDbi_1.52.0
## [17] knitr_1.31 DESeq2_1.30.1
## [19] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [21] MatrixGenerics_1.2.1 matrixStats_0.58.0
## [23] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
## [25] IRanges_2.24.1 S4Vectors_0.28.1
## [27] BiocGenerics_0.36.0
##
## loaded via a namespace (and not attached):
## [1] ggbeeswarm_0.6.0 colorspace_2.0-0 ellipsis_0.3.1
## [4] rprojroot_2.0.2 XVector_0.30.0 farver_2.1.0
## [7] bit64_4.0.5 fansi_0.4.2 xml2_1.3.2
## [10] splines_4.0.5 extrafont_0.17 cachem_1.0.4
## [13] jsonlite_1.7.2 Rsamtools_2.6.0 Rttf2pt1_1.3.8
## [16] dbplyr_2.1.1 compiler_4.0.5 httr_1.4.2
## [19] assertthat_0.2.1 Matrix_1.3-2 fastmap_1.1.0
## [22] htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.0.5
## [25] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4
## [28] maps_3.3.0 rappdirs_0.3.3 Rcpp_1.0.6
## [31] jquerylib_0.1.3 vctrs_0.3.7 Biostrings_2.58.0
## [34] ggalt_0.4.0 rtracklayer_1.50.0 extrafontdb_1.0
## [37] xfun_0.22 stringr_1.4.0 lifecycle_1.0.0
## [40] gtools_3.8.2 zlibbioc_1.36.0 MASS_7.3-53.1
## [43] scales_1.1.1 hms_1.0.0 proj4_1.0-10.1
## [46] yaml_2.2.1 curl_4.3 memoise_2.0.0
## [49] ggrastr_0.2.3 sass_0.3.1 stringi_1.5.3
## [52] RSQLite_2.2.6 highr_0.8 genefilter_1.72.1
## [55] caTools_1.18.2 BiocParallel_1.24.1 rlang_0.4.10
## [58] pkgconfig_2.0.3 bitops_1.0-6 evaluate_0.14
## [61] purrr_0.3.4 labeling_0.4.2 GenomicAlignments_1.26.0
## [64] bit_4.0.4 tidyselect_1.1.0 plyr_1.8.6
## [67] magrittr_2.0.1 R6_2.5.0 generics_0.1.0
## [70] DelayedArray_0.16.3 DBI_1.1.1 pillar_1.6.0
## [73] withr_2.4.1 survival_3.2-10 RCurl_1.98-1.3
## [76] ash_1.0-15 tibble_3.1.0 crayon_1.4.1
## [79] KernSmooth_2.23-18 utf8_1.2.1 BiocFileCache_1.14.0
## [82] rmarkdown_2.7 progress_1.2.2 locfit_1.5-9.4
## [85] blob_1.2.1 digest_0.6.27 xtable_1.8-4
## [88] openssl_1.4.3 munsell_0.5.0 beeswarm_0.3.1
## [91] vipor_0.4.5 bslib_0.2.4 askpass_1.1